[phenixbb] Different stats with different number of macrocycles

Phil Jeffrey pjeffrey at princeton.edu
Thu May 4 14:26:30 PDT 2017

But the variable weighting scheme that phenix.refine uses actually 
causes problems with this - the optimal weight(s) for cycle 1 is most 
assuredly not the optimal weight for cycles 2....n and it even does this 
with converged high resolution structures, so it's not just a result of 
the usual violence I do to structures when rebuilding them.

I think this trend of the first cycle weight being an outlier is quite 
possibly the source of what Pat is seeing, and it's not clear to me why 
phenix.refine does this where I see a lot less of it (if any at all) in 

Phil Jeffrey

On 5/4/17 2:36 PM, Schnicker, Nicholas J wrote:
> Hi Pat,
> I believe they suggest using target weight optimization in this case. It
> can be specified on the command line as below:
> optimize_xyz_weight=true  optimize_adp_weight=true
> I've found for a couple structures I had to use this or else the
> geometry was much worse. They also recommend to use this in the last
> round of refinement.
> Cheers,
> Nick

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